This week’s Spotlight is on Stephen Fried, founder of Microway and veteran technology inventor. Steve is a former space scientist and FAA flight examiner who can be found on weekends soaring in his sailplane over the Green Mountains of Vermont.

We caught up with Steve after learning that BioStack-LS — a CUDA/Tesla-based Microway product — was named "Best of Show" finalist at the Bio-IT World Conference in Boston this week. Here’s an extract from our interview:

Steve Fried in his Schleicher ASH-26 E sailplane

NVIDIA: Steve, tell us about Microway.

Steve: We develop x86-based Linux clusters whose nodes each employ a pair of NVIDIA Tesla GPUs. For the past four years, we’ve been providing customers with well-designed and cooled GPU platforms.

NVIDIA: Where are you seeing the most momentum in GPU computing?

Steve: Applications that manipulate matrices or rely on linear algebra techniques are excellent candidates for a system of parallel GPGPUs.

For example, we believe that GPUs are ideal for executing the parallel vector applications that dominate much of the bio-informatics world. This week we are at Bio-IT World demonstrating BioStack-LS. BioStack-LS includes seven GPU compute nodes, each with two Tesla C2070s.

BioStack-LS represents an innovation for the bio-medical community because it’s delivered pre-configured for life sciences software, including AMBER, MATLAB, NAMD and VMD.

NVIDIA: Why are people embracing the CUDA parallel programming model?

Steve: CUDA automatically solves many annoying problems.... It hides the bits and pieces of kernel control, data flow and task synchronization from the user. It reduces the user’s task to writing a single piece of C code that executes on the host, which automatically loads and calls the kernels that are embedded within the CUDA application in the order that they are to be executed....

The Keeneland Project is a five-year, $12 million grant awarded by the NSF for creation of an experimental high-performance system. Georgia Tech and its partners, the University of Tennessee at Knoxville and Oak Ridge National Lab, are deploying an HP system powered by Tesla GPUs. A Keeneland Workshop will be held April 14-15 in Atlanta.
- For more info, visit: http://keeneland.gatech.edu/
- Watch Prof. Jeff Vetter speak about Keeneland (SC09): http://is.gd/HuMNEr

NVIDIA’s Andy Walsh blogged this week about how OpenEye Scientific Software is tackling the challenges of drug discovery:

"A key path to drug discovery over the past decade has been the process of determining "shared bioactivity" between molecules, that is, determining the similarity of one molecule to another based on its three-dimensional shape.

There’s always been a catch, though. If you’re a large pharmaceutical company doing research in this area, you probably have a collection of more than a hundred million molecule shapes or conformations. In the rush to find new cures, how do you even begin to get through this much data in a reasonable timeframe, even in a lifetime?

Enter an innovative company called OpenEye Scientific Software, and its revolutionary new application called FastROCS."

CUDA is NVIDIA’s parallel computing hardware architecture. NVIDIA provides a complete toolkit for programming on the CUDA architecture, supporting standard computing languages such as C, C++ and Fortran as well as APIs such as OpenCL and DirectCompute. Send comments and suggestions to: cuda_week_in_review@nvidia.com

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